avrdude appears to be able to communicate with an ATxmega128A4U in PDI mode, but an attempt to program flash memory fails at verification; the memory appears to read back as 0xFF.

It looks like avrdude can read the flash correctly; if I program the chip using Atmel Studio, a quick glance at 'dump flash' in avrdude's terminal mode looks like an intact interrupt table. A chip erase from avrdude also appears to work; the flash reads back as 0xff after executing avrdude -e.

I captured the attached traces from Atmel Studio successfully programming (and then reading back) the flash memory. The hex file used is the appropriate xmega DFU bootloader image from AVR1916. The files were captured with Atmel Studio 6 running in VMware and wireshark on Linux capturing with the usbmon facility. I would be happy to capture additional operations if it would be useful.